SS is absolutely right - it is often said that it's two days after a hard effort that you feel the exhaustion most, rather than the day after when your body is still "pumped" up from having done well. I've certainly found this to be the case and plan for in these days - even though it still seems odd that it works that way.
Two things occur to me as well -
a) did you make sure to replenish carbs and fluids and most importantly proteins after your hard session? cos failing to do so adequately can have the effect of slowing you down. I've this year discovered the virtues of a protein supplement immediately after hard runs (especially long ones) and I mean immediately (i.e. within an hour or so at most) - I take a fairly pleasant milk chocolate type one from High5 which does the job for me.
b) the second point is did you cool-down sensibly after your hard work-out? Ten minutes gentle effort to flush the toxins out, and plenty of stretching makes all the difference to how well you're going to recover.
I can't comment on the stomach problem cos luckily I don't seem to get it (touch wood), but I think you're very sensible in looking at alternatives to Immodium.
Just feel good about your great work-out - I'm sure you'll be back to form in no time. Sadly, we can't always run as fast as our last best time every time we lace up our shoes, and usually it's your body's way of telling you to cut it a little slack! best. s.